New combinations, rank changes, and nomenclatural and taxonomic comments in the vascular flora of the southeastern United States. IV

Weakley, Alan S.; Sorrie, Bruce A.; LeBlond, Richard J.; Poindexter, Derick B.; Floden, Aaron; Schilling, Edward E.; Franck, Alan R.; Kees, John C.

doi:10.17348/jbrit.v12.i2.950

Cited by 4 publications

(6 citation statements)

References 9 publications

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“…Although only marginal, the 1272 tree had lower levels of discordance, indicating that 1272 provides better resolution at the nodes than 1061 (Figures 5 and 6), though the nodes are still highly discordant. It is reasonable to consider that these underlying biological processes may be influencing our concordance results as Packera members have a long history of reticulation (e.g., Bremer, 1994;Bain et al, 1997) and hybridizing in the wild (e.g., Fernald, 1943;Barkley, 1962;Chapman et al, 1971;Uttal, 1984;Bain, 1988;Trock, 1999;Gramling, 2006;Weakley et al, 2011). Similar conclusions have also been found in other groups (e.g., Sessa et al, 2012;Vargas et al, 2017;Morales-Briones et al, 2018).…”

Section: Discussionsupporting

confidence: 74%

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

Moore-Pollard

Jones

Mandel

2023

Preprint

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Premise: The sunflower family specific probe set, Compositae-1061, has enabled family-wide phylogenomic studies and investigations at lower-taxonomic levels by targeting 1,000+ genes. However, it generally lacks resolution at the genus to species level, especially in groups with complex evolutionary histories including polyploidy and hybridization. Methods: In this study, we developed a new HybSeq probe set, Compositae-ParaLoss-1272, designed to target orthologous loci in Asteraceae family members. We tested its efficiency across the family by simulating target-enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in genus Packera which has a complex evolutionary and taxonomic history. We performed HybSeq with Compositae-ParaLoss-1272 for 19 taxa which were previously studied using the Compositae-1061 probe set. Sequences from both probe sets were used to generate phylogenies, compare topologies, and assess node support. Results: We report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members. Additionally, Compositae-ParaLoss-1272 had less gene tree discordance, recovered considerably fewer paralogous sequences, and retained longer loci than Compositae-1061. Discussion: Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate this new probe set will provide improved resolution and utility for studies at lower-taxonomic levels and complex groups in the sunflower family.

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Section: Discussionsupporting

confidence: 74%

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

Moore-Pollard

Jones

Mandel

2023

Preprint

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“…Gmel.) H. Hebert (Wunderlin & Hansen 2001;Orzell & Bridges 2002), until its recent re-recognition at species level as Trilisa subtropicana within a more narrowly circumscribed genus (Orzell & Bridges 2017). Compared to Carphephorus, Trilisa and Litrisa have smaller heads (involucres 3.5-6 mm high), fewer phyllaries per head (5-12), lack recaptacular paleae, and have leaves either bearing punctate glands in Litrisa or without any shining resin dots in Trilisa (Nesom 2006;Weakley & Southeastern Flora Team 2022).…”

Section: Alleged Southern D Umbellatamentioning

confidence: 99%

“…Additional supporting specimens have been observed as far north as Polk County (Corogin SB215, FLAS), and Sumter County (Baltzell 2746, FLAS). Specifically, T. subtropicana has been shown to be distinct from T. odoratissima based on a mostly defined geographic separation in central and southern Florida, an absence of coumarin or vanilla odor, shorter and thinner basal leaves (less than 15 cm long; less than 5 cm wide), stem leaves entire, more elliptic, and tightly clasping the stem, involucres more densely viscid, inflorescences broader than tall, and the primary inflorescence branches diverging at a wider, more arcuate angle (Delaney et al 1999;Orzell & Bridges 2002;Orzell & Bridges 2017;Figs. 2, 3).…”

Section: Alleged Southern D Umbellatamentioning

confidence: 99%

“…Despite considerable efforts on the Trilisa subtropicana/T. odoratissima complex in Florida (Delaney et al 1999;Orzell & Bridges 2002;Orzell & Bridges 2017), and research into hybrid genera in the Liatrinae (Schilling 2011), no mention has been made of hybrids between Trilisa species. Additional surveys are needed to search for hybrids across the sympatric range of T. subtropicana and T. paniculata, and further surveys for potential hybrids between the much more widespread and overlapping Trilisa odoratissima and Trilisa paniculata would probably increase our overall knowledge of hybridization within Trilisa in the Southeastern Coastal Plain.…”

Section: Alleged Southern D Umbellatamentioning

confidence: 99%

“…The stem leaves and inflorescence bracts of T. subtropicana and T. ×subpaniculata are both more noticeably reduced compared to the only moderately reduced upper leaves and bracts of T. paniculata. All descriptions of the peduncles of Trilisa subtropicana and Trilisa odoratissima (basionym Carphephorus odoratissimus) are specified as glabrous (Delaney et al 1999;Orzell & Bridges 2002;Nesom 2006;Orzell & Bridges 2017)…”

Section: Trilisa ×Subpaniculatamentioning

confidence: 99%

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Studies in the vascular flora of the southeastern United States. VIII

Weakley¹,

Poindexter²,

Sorrie³

et al. 2022

J. Bot. Res. Inst. Texas

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As part of ongoing efforts to understand, document, and conserve the flora of the southeastern United States, we make new combinations to accord with our generic taxonomy, name a new hybrid, re-recognize a species relegated to synonymy in recent decades, lectotypify and generally clarify nomenclatural issues in several genera, clarify taxonomy and distributions of species, and report important new and current distribution records. In Doellingeria (Asteraceae), we clarify the taxonomy and distribution of D. sericocarpoides and D. umbellata in the region. In Trilisa (Asteraceae), we summarize and clarify the taxonomy, name a new hybrid, and present a new key to the taxa in the genus. Species delimitation in Stillingia (Euphorbiaceae) has been controversial and unsettled in the region, and we examine the confused taxonomy and nomenclature of the genus in the southeastern United States, re-recognizing a species used by J.K. Small, but with an expanded circumscription and a clarification of various nomenclatural issues. We examine typification of Desmodium dillenii (Fabaceae) and its application to our modern understanding of the circumscription of taxa, recommending it be considered a junior synonym of Desmodium glabellum. In Juncus, we assign a lectotype for Juncus anthelatus, fixing its application. In Primulaceae, we discuss the delineation of genera in Lysimachieae, and take a middle path regarding lumping/splitting, supporting the recognition of traditional and monophyletic segregates Trientalis, Steironema, Anagallis, and Centunculus, while treating Lysimachia in a moderately broad sense, including Glaux and multiple subclades; in order to implement this taxonomy in the southeastern United states, we make a single new combination in Steironema. We also discuss generic circumscription in Selaginellaceae, and argue for the recognition at genus rank of six major clades, monophyletic, ancient, and morphologically recognizable; in order to apply this taxonomy in the southeastern United States, we make five new combinations in Bryodesma, Gymnogynum, and Stachygynandrum. Finally, we report important new records of locally, regionally, or globally rare species in North Carolina: Helanthium tenellum, Chenopodium berlandieri var. macrocalycium, Carex barrattii, Carex vestita, Eleocharis compressa var. compressa, Rhynchospora compressa, Rhynchospora sulcata, and Croton michauxii.

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Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems

Moore‐Pollard,

Jones,

Mandel

2024

Appl Plant Sci

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PremiseA family‐specific probe set for sunflowers, Compositae‐1061, enables family‐wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization.MethodsWe developed a Hyb‐Seq probe set, Compositae‐ParaLoss‐1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus Packera. We performed Hyb‐Seq with Compositae‐ParaLoss‐1272 for 19 Packera taxa that were previously studied using Compositae‐1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support.ResultsWe report that Compositae‐ParaLoss‐1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae‐1061. Most notably, Compositae‐ParaLoss‐1272 recovered substantially fewer paralogous sequences than Compositae‐1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae‐1061.DiscussionGiven the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae‐ParaLoss‐1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.

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New combinations, rank changes, and nomenclatural and taxonomic comments in the vascular flora of the southeastern United States. IV

Cited by 4 publications

References 9 publications

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

Studies in the vascular flora of the southeastern United States. VIII

Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems

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